The functional properties of tissues are governed by physical and chemical processes occurring at cellular and subcellular length scales. Specifically, the physical state of tissues (e.g., osmotic and mechanical properties, state of hydration, charge density) must be characterized on length scales below 100 nm. Understanding the interaction of polyelectrolytes with ions is critical to clarifying the basic physics of ion binding as well as physical mechanisms affecting a large number of biological processes. The action of ions is complex: they stabilize local structures, and can also affect the intrinsic properties of the polymer chain, such as its flexibility, electrostatic interactions and the overall thermodynamics of the system. To determine the effect of ions on the structure and dynamic properties of biopolymers we developed a multi-scale experimental framework by combining scattering techniques, such as small-angle X-ray scattering (SAXS), small-angle neutron scattering (SANS), and static light scattering (SLS), with macroscopic methods (osmotic swelling pressure and mechanical measurements). We also use dynamic methods e.g., neutron spin echo (NSE), dynamic light scattering (DLS) to observe the relaxation response as a function of length scale. Additionally, we developed a method to determine the distribution of counterions in the ionic atmosphere surrounding charged macromolecules using anomalous small-angle X-ray scattering (ASAXS). In biology, osmotic pressure is particularly important in regulating and mediating physiological processes. Swelling pressure measurements probe the system in the large length scale range, thus providing information on the overall thermodynamic response. SANS and SAXS allow us to investigate biopolymer molecules and assemblies in their natural environment and to correlate the changes in the environmental conditions (e.g., ion concentration, ion valance, pH, temperature) with physical properties such as molecular conformation and osmotic pressure. These techniques simultaneously provide information about the size of different structural elements and their respective contribution to the osmotic properties. Combining these measurement techniques allows us to determine the length scales governing the macroscopic thermodynamic properties. It is important to emphasize that this information cannot be obtained by other techniques. We have studied the effect of multivalent cations, particularly calcium ions, on the structure of various model systems mimicking soft tissues. Divalent cations are ubiquitous in the biological milieu, yet existing theories do not adequately explain their effect on and interactions with charged macromolecules. Moreover, experiments to study these interactions are difficult to perform, particularly in solution, because above a low ion concentration threshold multivalent cations generally cause phase separation or precipitation of charged macromolecules. We have overcome this limitation by cross-linking our biopolymers into gels. This procedure greatly extends the range of ion concentrations over which the system remains stable. In previous studies, we have investigated cross-linked gels of a model synthetic polymer, polyacrylic acid, and different biopolymers such as DNA, hyaluronic acid and chondroitin sulfate (important components of extracellular matrix) to determine the size of the structural elements that contribute to the osmotic concentration fluctuations. We have combined SANS and SAXS to estimate the osmotic modulus of hyaluronic acid solutions and gels in the presence of monovalent and divalent counterions. We studied the collective diffusion processes in these solutions by dynamic light scattering and determined the osmotic modulus from the relaxation response. We determined the distribution of counterions around charged biopolymer molecules using anomalous small-angle X-ray scattering measurements. We applied our approach to understand the binding mechanism in glucose sensors made from smart zwitterionic hydrogels containing boronic acid moieties. Based on systematic SANS and osmotic pressure measurements we provided a thermodynamic explanation for the enhanced selectivity of these gels for glucose relative to fructose. This class of material has a great potential in the development of implantable continuous glucose sensors for use in managing diabetes. We developed a procedure to control the size, compactness and stability of DNA nanoparticles by mediating the interaction between ions and DNA. We quantified the effects of salt, pH and temperature on their stability and biological activity. These polyplexes are pathogen-like particles having a size (70 - 300 nm) and shape resembling spherical viruses that naturally evolved to deliver nucleic acids to cells. They contain pDNA in the interior surrounded by synthetic polymer presenting sugar residues on the surface recognized by M cells and dendritic cells as pathogens. Because we can control the stability and biological activity of DNA nanoparticles, we believe that this knowledge can provide a solid foundation for developing new DNA-based vaccines for the treatment of various diseases. We studied the effect of calcium ions on the larger scale structure of DNA solutions and gels in near-physiological salt conditions by SANS. Analysis of the SANS response revealed two characteristic length scales, the mesh size of the transient network, and the cross-sectional radius of the DNA double helix. In gels the mesh size is greater than in the corresponding solutions by approximately 50%, reflecting the increased heterogeneity of the crosslinked system. The cross-sectional radius of the DNA chain is practically independent of the polymer concentration and the calcium ion content, and is close to the value of the DNA double helix (10 A). This finding implies that bundle formation is negligible in these DNA gels. The results of this study show that changes in the ionic environment offer a molecular level control of the interactions between DNA strands and allow us to tune the morphology of DNA-based assemblies. In recent studies we have investigated the mechanism of fiber formation from small hydrogelator molecules in biological cells. Fluorescent imaging revealed that self-assembly directly affects the distribution of small peptidic molecules in the cellular environment. Cell viability tests suggested that the states and the spatial distribution of the molecular assemblies control the phenotypes of the cells. We demonstrated that enzyme instructed self-assembly makes it possible to modulate the spatiotemporal profiles of small molecules in a cellular environment. We have developed an in situ tumor-specific formation of self-assemblies to enrich indocyanin green (ICG) for fluorescence/photoacoustic dual-modality imaging guided photothermal therapy (PTT). Due to the intermolecular interaction between peptide and ICG, ICG molecules are spontaneously doped into nanofibers by head-to-tail arrangement. The ICG-doped nanofiber exhibits enhanced NIR absorbance, partially quenched fluorescence emission, and unique photoacoustic and photothermal properties. The cancer theranostic capability of ICG-Nanofiber was carefully investigated both in vitro and in vivo. This study is important because it provides a novel concept of in situ tumor-specific formation of NPs that can potentially be applied to deliver diagnostic/therapeutic agents. In addition, it also paves the way toward the goal of personalized medicine by endogenous stimuli instructed construction of functional nanostructures for clinical translatable PTT theranostics, or guidance of surgical resection.